Filling
Updated
The step where a good batch becomes a set of products, and where contamination is introduced if it is going to be.
Fill by weight
The label declares a net quantity, and for a liquid that is usually a volume, which you deliver most reliably by weighing, because a scale is more accurate than a sight line and does not care about foam.
Establish the target fill weight by filling and weighing several bottles, then hold it.
Check periodically through a run rather than at the start, because a gravity filler slows as the reservoir empties.
Headspace
Enough that the product can expand with temperature without stressing the closure, and that a trigger dip tube has somewhere to sit.
Too little and a warm delivery van produces leaking closures.
Too much and the bottle looks under-filled, which customers notice, and there is more air in contact with the product.
Keeping it clean
This is the contamination step, and a preservative can only cope with so much.
Sanitize the filling equipment, the tubing and any reservoir before a run, and do not leave product standing in tubing between runs.
New bottles are not sterile. For a product with any microbial sensitivity, it is worth knowing how yours are stored and shipped.
And keep the filling area separate from where raw materials are handled.
Capping
To a consistent torque. Under-tightened leaks; over-tightened strips the thread or distorts the liner so it leaks anyway.
A torque gauge is cheap and it removes a common cause of a leaking parcel.
Check the closure is the right one for the formula, which is a compliance question where a child-resistant closure is required.
And inspect along the finished row: fill level, cap seating, label position, anything on the outside of the bottle.